[Chimera-users] How can one create a sculpted view of a cellular assembly?

Kenward Vaughan kay_jay at earthlink.net
Wed Jan 21 23:08:46 PST 2015

On 01/21/2015 12:15 PM, Tom Goddard wrote:
> Hi Kenward,
>    As Elaine points out you can do some fancy cut open views in Chimera
> now, although the user interface is difficult — requires that you know a
> lot about Chimera.  I’ve attached 3 images of the cellPACK HIV model cut
> open and here are the commands I used to do it.

Thank you both for the pointers and examples of approaches for doing this.

I had not paid attention to the information about the objects being 
surfaces for Chimera.  After assimilating Tom's suggested commands and 
playing a bit, what was created fits what I am looking for, and I'm 
ready to play further to expand on it.  Some of the selection methods 
Elaine suggested will help with that.

Thank you so much with this!  I expect I may have a few more questions 
down the line, and appreciate knowing the tremendous resource you folks 
represent to me and others using this wonderful software.


>> On Jan 21, 2015, at 8:51 AM, Elaine Meng  wrote:
>> Hi Kenward,
>> Those suggestions all make sense for exploring and displaying a
>> multicomponent structure.  In fact, the cellpack.org
>> <http://cellpack.org> “use” page shows an HIV model depicted in other
>> software that shows some of your suggested features:
>> <http://www.cellpack.org/use>
>> This page also lists the available Cellpack models that you can open
>> with Fetch by ID in Chimera 1.10.1 or daily build. Currently just
>> HIV-1_0.1.6_6 but we expect additional ones soon.
>> Chimera does have some capabilities along the lines of your
>> suggestions, but not fully.  Here’s what it has now (others, please
>> chime in if I forgot anything):

>> On Jan 20, 2015, at 11:32 PM, Kenward Vaughan wrote:
>>> As I slowly approach the operational realization of my
>>> computational/visualization lab, I received your lovely holiday card.
>>> This seriously elevated my dreams of larger scale possibilities for
>>> chemistry and biology students through the cellPack resources.
>>> In playing with it, I found myself wanting a more robust version of a
>>> clipping plane which would have several characteristics:
>>> 3 dimensional - take a cell and hack out 1 or 2 adjoining octants

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